deprecated old multivariate functions

with the new interface, the previous functions for computing multivariate
profiles and distances are obsolete. This is now noted in the docs.

3 files changed, 77 insertions, 60 deletions

diff --git a/pyspike/isi_distance.py b/pyspike/isi_distance.py
index 122e11d..e91dce2 100644
--- a/pyspike/isi_distance.py
+++ b/pyspike/isi_distance.py
@@ -20,14 +20,22 @@ def isi_profile(*args, **kwargs):
 
     Valid call structures::
 
-      isi_profile(st1, st2)  # returns the bi-variate profile
+      isi_profile(st1, st2)       # returns the bi-variate profile
       isi_profile(st1, st2, st3)  # multi-variate profile of 3 spike trains
 
       spike_trains = [st1, st2, st3, st4]  # list of spike trains
-      isi_profile(spike_trains)  # profile of the list of spike trains
+      isi_profile(spike_trains)   # profile of the list of spike trains
       isi_profile(spike_trains, indices=[0, 1])  # use only the spike trains
                                                  # given by the indices
 
+    The multivariate ISI distance profile for a set of spike trains is defined
+    as the average ISI-profile of all pairs of spike-trains:
+
+    .. math:: <I(t)> = \\frac{2}{N(N-1)} \\sum_{<i,j>} I^{i,j},
+
+    where the sum goes over all pairs <i,j>
+
+
     :returns: The isi-distance profile :math:`I(t)`
     :rtype: :class:`.PieceWiseConstFunc`
     """
@@ -43,10 +51,9 @@ def isi_profile(*args, **kwargs):
 # isi_profile_bi
 ############################################################
 def isi_profile_bi(spike_train1, spike_train2):
-    """ Bi-variate ISI-profile.
-    Computes the isi-distance profile :math:`I(t)` of the two given
-    spike trains. Returns the profile as a PieceWiseConstFunc object.
-    See :func:`.isi_profile`.
+    """ Specific function to compute a bivariate ISI-profile. This is a
+    deprecated function and should not be called directly. Use
+    :func:`.isi_profile` to compute ISI-profiles.
 
     :param spike_train1: First spike train.
     :type spike_train1: :class:`.SpikeTrain`
@@ -85,12 +92,10 @@ Falling back to slow python backend.")
 # isi_profile_multi
 ############################################################
 def isi_profile_multi(spike_trains, indices=None):
-    """ computes the multi-variate isi distance profile for a set of spike
-    trains. That is the average isi-distance of all pairs of spike-trains:
+    """ Specific function to compute the multivariate ISI-profile for a set of
+    spike trains. This is a deprecated function and should not be called
+    directly. Use :func:`.isi_profile` to compute ISI-profiles.
 
-    .. math:: <I(t)> = \\frac{2}{N(N-1)} \\sum_{<i,j>} I^{i,j},
-
-    where the sum goes over all pairs <i,j>
 
     :param spike_trains: list of :class:`.SpikeTrain`
     :param indices: list of indices defining which spike trains to use,
@@ -115,6 +120,14 @@ def isi_distance(*args, **kwargs):
 
     .. math:: D_I = \\int_{T_0}^{T_1} I(t) dt.
 
+    In the multivariate case it is the integral over the multivariate
+    ISI-profile, i.e. the average profile over all spike train pairs:
+
+    .. math:: D_I = \\int_0^T \\frac{2}{N(N-1)} \\sum_{<i,j>} I^{i,j},
+
+    where the sum goes over all pairs <i,j>
+
+
 
     Valid call structures::
 
@@ -139,14 +152,12 @@ def isi_distance(*args, **kwargs):
 
 
 ############################################################
-# isi_distance_bi
+# _isi_distance_bi
 ############################################################
 def isi_distance_bi(spike_train1, spike_train2, interval=None):
-    """ Computes the ISI-distance :math:`D_I` of the given spike trains. The
-    isi-distance is the integral over the isi distance profile
-    :math:`I(t)`:
-
-    .. math:: D_I = \\int_{T_0}^{T_1} I(t) dt.
+    """ Specific function to compute the bivariate ISI-distance.
+    This is a deprecated function and should not be called directly. Use
+    :func:`.isi_distance` to compute ISI-distances.
 
     :param spike_train1: First spike train.
     :type spike_train1: :class:`.SpikeTrain`
@@ -181,12 +192,9 @@ def isi_distance_bi(spike_train1, spike_train2, interval=None):
 # isi_distance_multi
 ############################################################
 def isi_distance_multi(spike_trains, indices=None, interval=None):
-    """ computes the multi-variate isi-distance for a set of spike-trains.
-    That is the time average of the multi-variate spike profile:
-
-    .. math:: D_I = \\int_0^T \\frac{2}{N(N-1)} \\sum_{<i,j>} I^{i,j},
-
-    where the sum goes over all pairs <i,j>
+    """ Specific function to compute the multivariate ISI-distance.
+    This is a deprecfated function and should not be called directly. Use
+    :func:`.isi_distance` to compute ISI-distances.
 
     :param spike_trains: list of :class:`.SpikeTrain`
     :param indices: list of indices defining which spike trains to use,
diff --git a/pyspike/spike_distance.py b/pyspike/spike_distance.py
index 7acb959..0fd86c1 100644
--- a/pyspike/spike_distance.py
+++ b/pyspike/spike_distance.py
@@ -28,6 +28,13 @@ def spike_profile(*args, **kwargs):
       spike_profile(spike_trains, indices=[0, 1])  # use only the spike trains
                                                    # given by the indices
 
+    The multivariate spike-distance profile is defined as the average of all
+    pairs of spike-trains:
+
+    .. math:: <S(t)> = \\frac{2}{N(N-1)} \\sum_{<i,j>} S^{i, j}`,
+
+    where the sum goes over all pairs <i,j>
+
     :returns: The spike-distance profile :math:`S(t)`
     :rtype: :class:`.PieceWiseConstLin`
     """
@@ -43,9 +50,9 @@ def spike_profile(*args, **kwargs):
 # spike_profile_bi
 ############################################################
 def spike_profile_bi(spike_train1, spike_train2):
-    """ Computes the spike-distance profile :math:`S(t)` of the two given spike
-    trains. Returns the profile as a PieceWiseLinFunc object. The SPIKE-values
-    are defined positive :math:`S(t)>=0`.
+    """ Specific function to compute a bivariate SPIKE-profile. This is a
+    deprecated function and should not be called directly. Use
+    :func:`.spike_profile` to compute SPIKE-profiles.
 
     :param spike_train1: First spike train.
     :type spike_train1: :class:`.SpikeTrain`
@@ -86,12 +93,9 @@ Falling back to slow python backend.")
 # spike_profile_multi
 ############################################################
 def spike_profile_multi(spike_trains, indices=None):
-    """ Computes the multi-variate spike distance profile for a set of spike
-    trains. That is the average spike-distance of all pairs of spike-trains:
-
-    .. math:: <S(t)> = \\frac{2}{N(N-1)} \\sum_{<i,j>} S^{i, j}`,
-
-    where the sum goes over all pairs <i,j>
+    """ Specific function to compute a multivariate SPIKE-profile. This is a
+    deprecated function and should not be called directly. Use
+    :func:`.spike_profile` to compute SPIKE-profiles.
 
     :param spike_trains: list of :class:`.SpikeTrain`
     :param indices: list of indices defining which spike trains to use,
@@ -128,6 +132,13 @@ def spike_distance(*args, **kwargs):
       spike_distance(spike_trains, indices=[0, 1])  # use only the spike trains
                                                     # given by the indices
 
+    In the multivariate case, the spike distance is given as the integral over
+    the multivariate profile, that is the average profile of all spike train
+    pairs:
+
+    .. math::  D_S = \\int_0^T \\frac{2}{N(N-1)} \\sum_{<i,j>}
+               S^{i, j} dt
+
     :returns: The spike-distance :math:`D_S`.
     :rtype: double
     """
@@ -144,11 +155,9 @@ def spike_distance(*args, **kwargs):
 # spike_distance_bi
 ############################################################
 def spike_distance_bi(spike_train1, spike_train2, interval=None):
-    """ Computes the spike-distance :math:`D_S` of the given spike trains. The
-    spike-distance is the integral over the spike distance profile
-    :math:`S(t)`:
-
-    .. math:: D_S = \int_{T_0}^{T_1} S(t) dt.
+    """ Specific function to compute a bivariate SPIKE-distance. This is a
+    deprecated function and should not be called directly. Use
+    :func:`.spike_distance` to compute SPIKE-distances.
 
     :param spike_train1: First spike train.
     :type spike_train1: :class:`.SpikeTrain`
@@ -183,13 +192,9 @@ def spike_distance_bi(spike_train1, spike_train2, interval=None):
 # spike_distance_multi
 ############################################################
 def spike_distance_multi(spike_trains, indices=None, interval=None):
-    """ Computes the multi-variate spike distance for a set of spike trains.
-    That is the time average of the multi-variate spike profile:
-
-    .. math::  D_S = \\int_0^T \\frac{2}{N(N-1)} \\sum_{<i,j>}
-               S^{i, j} dt
-
-    where the sum goes over all pairs <i,j>
+    """ Specific function to compute a multivariate SPIKE-distance. This is a
+    deprecated function and should not be called directly. Use
+    :func:`.spike_distance` to compute SPIKE-distances.
 
     :param spike_trains: list of :class:`.SpikeTrain`
     :param indices: list of indices defining which spike trains to use,
diff --git a/pyspike/spike_sync.py b/pyspike/spike_sync.py
index ccb09d9..617dd86 100644
--- a/pyspike/spike_sync.py
+++ b/pyspike/spike_sync.py
@@ -34,6 +34,11 @@ def spike_sync_profile(*args, **kwargs):
       spike_sync_profile(sts, indices=[0, 1])  # use only the spike trains
                                                # given by the indices
 
+    In the multivariate case, the profile is defined as the number of
+    coincidences for each spike in the set of spike trains divided by the
+    number of spike trains pairs involving the spike train of containing this
+    spike, which is the number of spike trains minus one (N-1).
+
     :returns: The spike-sync profile :math:`S_{sync}(t)`.
     :rtype: :class:`pyspike.function.DiscreteFunction`
     """
@@ -49,10 +54,9 @@ def spike_sync_profile(*args, **kwargs):
 # spike_sync_profile_bi
 ############################################################
 def spike_sync_profile_bi(spike_train1, spike_train2, max_tau=None):
-    """ Computes the spike-synchronization profile S_sync(t) of the two given
-    spike trains. Returns the profile as a DiscreteFunction object. The S_sync
-    values are either 1 or 0, indicating the presence or absence of a
-    coincidence.
+    """ Specific function to compute a bivariate SPIKE-Sync-profile. This is a
+    deprecated function and should not be called directly. Use
+    :func:`.spike_sync_profile` to compute SPIKE-Sync-profiles.
 
     :param spike_train1: First spike train.
     :type spike_train1: :class:`pyspike.SpikeTrain`
@@ -98,11 +102,9 @@ Falling back to slow python backend.")
 # spike_sync_profile_multi
 ############################################################
 def spike_sync_profile_multi(spike_trains, indices=None, max_tau=None):
-    """ Computes the multi-variate spike synchronization profile for a set of
-    spike trains. For each spike in the set of spike trains, the multi-variate
-    profile is defined as the number of coincidences divided by the number of
-    spike trains pairs involving the spike train of containing this spike,
-    which is the number of spike trains minus one (N-1).
+    """  Specific function to compute a multivariate SPIKE-Sync-profile.
+    This is a deprecated function and should not be called directly. Use
+    :func:`.spike_sync_profile` to compute SPIKE-Sync-profiles.
 
     :param spike_trains: list of :class:`pyspike.SpikeTrain`
     :param indices: list of indices defining which spike trains to use,
@@ -176,6 +178,9 @@ def spike_sync(*args, **kwargs):
       spike_sync(spike_trains, indices=[0, 1])  # use only the spike trains
                                                 # given by the indices
 
+    The multivariate SPIKE-Sync is again defined as the overall ratio of all
+    coincidence values divided by the total number of spikes.
+
     :returns: The spike synchronization value.
     :rtype: `double`
     """
@@ -192,11 +197,9 @@ def spike_sync(*args, **kwargs):
 # spike_sync_bi
 ############################################################
 def spike_sync_bi(spike_train1, spike_train2, interval=None, max_tau=None):
-    """ Computes the spike synchronization value SYNC of the given spike
-    trains. The spike synchronization value is the computed as the total number
-    of coincidences divided by the total number of spikes:
-
-    .. math:: SYNC = \sum_n C_n / N.
+    """ Specific function to compute a bivariate SPIKE-Sync value.
+    This is a deprecated function and should not be called directly. Use
+    :func:`.spike_sync` to compute SPIKE-Sync values.
 
     :param spike_train1: First spike train.
     :type spike_train1: :class:`pyspike.SpikeTrain`
@@ -219,8 +222,9 @@ def spike_sync_bi(spike_train1, spike_train2, interval=None, max_tau=None):
 # spike_sync_multi
 ############################################################
 def spike_sync_multi(spike_trains, indices=None, interval=None, max_tau=None):
-    """ Computes the multi-variate spike synchronization value for a set of
-    spike trains.
+    """ Specific function to compute a multivariate SPIKE-Sync value.
+    This is a deprecated function and should not be called directly. Use
+    :func:`.spike_sync` to compute SPIKE-Sync values.
 
     :param spike_trains: list of :class:`pyspike.SpikeTrain`
     :param indices: list of indices defining which spike trains to use,